Nakano developed through Japan's domestic motorcycle championships, becoming the All-Japan 250cc champion in 1998. He moved to international competition full-time in 1999, adapting quickly to 250cc Grand Prix racing and finishing fourth overall with five podium finishes. The following year, 2000, was a close three-way battle for the championship; his teammate Olivier Jacque ultimately claimed the title while Nakano and Daijiro Kato contested the minor positions. Nakano also set the fastest 250cc lap at Motegi that year, a record that stood until 2008 — the longest-running lap record in the series at that time.
When the Tech 3 team stepped up to the 500cc class for 2001, Nakano moved with them. Despite competitive machinery, he could manage only fifth in the championship. He entered 2002 on a 500cc two-stroke before the team acquired a 990cc four-stroke machine later in the season as MotoGP's new era took hold.
In 2003 results were disappointing, prompting a move to Kawasaki for 2004. The Japanese manufacturer had suffered a troubled debut in MotoGP with Garry McCoy and Andrew Pitt, but improved noticeably with Nakano aboard. Kawasaki achieved their first MotoGP podium at the 2004 Japanese Grand Prix, and Nakano delivered two consecutive tenth-place championship finishes across 2004 and 2005, representing meaningful progress for the team.
The 2006 season highlighted a characteristic of Nakano's Kawasaki period: strong qualifying on Bridgestone tyres that did not always translate into race results. He was penalised twice for jump starts that season. At the Australian Grand Prix he started from the front row, led the early laps, but switched to wet tyres too late when conditions changed and could not recover competitive pace.
For 2007, Nakano joined the Konica Minolta Honda team. Results were thin across the season, with only occasional top-ten finishes in qualifying and races. In 2008 he moved to the Gresini Honda team, replacing Toni Elías, and benefited from the combination of his experience with Bridgestone tyres and Honda machinery. He scored more championship points in the first half of 2008 than in the whole of 2007. At Brno, he was given access to a factory-specification spring-valve Honda RC212V, which produced a string of significantly improved results. However, the Gresini team signed Elías again for 2009 and Nakano left at the season's end.
For 2009, Aprilia signed Nakano alongside Max Biaggi for their return to the Superbike World Championship after a three-year absence. The season was disrupted by injury — a broken collarbone and a subsequent neck injury kept him out of the final three rounds. He finished fourteenth in the championship. On October 28, 2009, Nakano announced his retirement from professional motorcycle racing.
Shinya Nakano spent the longest portion of his MotoGP career as a consistent mid-field competitor who occasionally demonstrated front-running pace, most visibly at Kawasaki in 2004 and with the Gresini team in 2008. His decade in world championship competition, from the 250cc class in 1999 through MotoGP in 2008, made him one of the more durable Japanese riders of his generation in international Grand Prix racing. His long-standing 250cc lap record at Motegi — unbroken for eight years — reflects the quality of his performance in that category early in his career.